Shell molecular dynamics#
GROMACS can simulate polarizability using the shell model of Dick and
Overhauser 43. In such models a shell particle
representing the electronic degrees of freedom is attached to a nucleus
by a spring. The potential energy is minimized with respect to the shell
position at every step of the simulation (see below). Successful
applications of shell models in GROMACS have been published for
Optimization of the shell positions#
The force
where
In an iterative solver, we have positions
and the optimal position for the shells
if we write
we finally obtain
which then yields the algorithm to compute the next trial in the optimization of shell positions